Cipher: 2605
Nomenclature: Functional genomics
Study programme: Molecular biosciences
Module: Biomedicine
Case holder:

Assoc. prof.dr.sc. Marijeta Kralj, zn. Advisor-permanent choice
Institution of the case holder:

Rudjer Boskovic Institute, Department of Molecular Medicine
Contributors - Contractors:
Subject status: Electoral College
The year in which the case is submitted: Year I
The semester in which the case is submitted: Semester II
Subject objective:

To know modern technology in the analysis of expression and function of genes and proteins, the importance of computer data processing (bioinformatics) and the huge possibilities of using these methods in basic research, diagnosis, prognostication and discovery of new drugs. To raise awareness of the need for interdisciplinary research and computer data processing.
Case contents:

Functional genomics is based on experiments involving the analysis of a wide range of genes and/or proteins and computer analysis of the results obtained. The main strategy of work in the field of functional genomics is to expand the range of research of a biological sample so that from the analysis of a particular gene (protein), it moves from the analysis of a particular gene (protein), to a systematic study of the activities of a multitude of them at once. Functional genomics aim to consolidate and link the information that gene sequences give us with its function, all in order to gain insight into the processes of a biological system.
Topics: Introduction to functional genomics, DNA chip technology, basic principles of proteomics, overview of techniques used in proteomics with special emphasis on "differential" profiling, protein identification and post-translation modifications, gene discovery in healthy organisms and in sick states, determination of gene function, gene and target therapy, pharmacogenomics and toxicogenomics, molecular portraits of cancer, molecular portraits of cancer responses, molecular portraits of cancer responses, importance of bioinformatics.
Learning outcomes: competences, knowledge, skills that the subject develops:

1. Explain the basic concepts in the functional genomics, such as genomics, proteomics, metabolomics, chemokenomics.
2. Anticipate the possibilities of using new technologies of a wide range in the investigation of cell functions in health and disease, in the analysis of the expression and function of genes and proteins, or in the process of discovering the drug.
3. Analyze the molecular aspects and regulation of gene and protein expression.
4. Train to work on state-of-the-art equipment (microchips, next generation sequencing, NGS)
5. Review ways of researching biomarkers and the importance of personalised medicine.
ECTS Credits 3
Lectures 5
Seminars (IS) 5
Exercises (E) 5
Altogether 15
The way of teaching and acquiring knowledge:

regular attendance and compulsory attendance of exercises
Ways of teaching and acquiring knowledge: (notes)
Monitoring and evaluating students (mark in fat printing only relevant categories) Attendance, Mandatory seminar work
Rating method: Written exam
Mandatory literature:

Recent scientific publications (scientific and review articles) covering the field of functional genomics will be used.
1. Young RA. Biomedical discovery with DNA arrays. Cell, 102:9-15, 2000.
2.C. Hultschig, J.Kreutzberger, H. Seitz, Z. Konthur, K. Bussow, H. Lehrach. Recent advances of protein microarrays. Current Opinion in Chemical Biology 2006, 10:4–10.
3. Pandey A, Mann M. Proteomics to study genes and genomes. Nature, 405:837-846, 2000.
4. Modelska A., Quattrone A., Re A.: Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Briefings in Bioinformatics, 2015, 1–8.
5. Stunnenberg H. G., Hubner N.C. Genomics meets proteomics: identifying the culprits in disease. Hum Genet (2014) 133:689–700.
6. Bredel M., Jacoby E.. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nature Rev Genet (2004) 5:262-275.
7.M. Baker. The 'omes puzzle. Nature (2013) 474:416-419.
Supplementary (recommended) literature:

1. Macgregor PF, Squire JA. Application of microarrays to the analysis of gene expression in cancer. It's Clin. Chem. 48:1170-1177, 2002.
2. Mohr S, Leikauf GD, Keith G. Rihn BH. Microarrays as cancer keys: an array of possibilities. J. Clin. Oncol. 20:3165-3175, 2002.
3. V. Kulasingam and E. P Diamandis. Strategies for discovering novel cancer biomarkers through utilization of emerging technologies. Nature clinical practice oncology (2008) 5:588-599.
4. Steven W. Cole. Human Social Genomics. PLOS Genomics (2014) e1004601.
How to monitor the quality and performance performance (evaluation):

The success of the course will be evaluated annually by the joint expert committee of the Rudjer Boskovic Institute, the University of Dubrovnik and the University of Osijek, and the leaders will receive information from the participants about the adequacy of the program and performance by the leadership through the survey.